X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6NIE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2291Equal volumes of protein solution (SwHalB (2.5 mg/ml), lysine (3 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (succinate phosphate glycine (SPG) buffer (100 mM, pH 5.2), 18% (w/v) PEG 1500) were mixed
Crystal Properties
Matthews coefficientSolvent content
3.6466.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.48α = 90
b = 165.48β = 90
c = 105.332γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray194PIXELDECTRIS PILATUS3 S 6M2018-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.05143.4199.8123.939.6553826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.197.30.7061.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6NIE2.0582.741.3353747277499.780.19860.19730.223147.3102
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3829
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms27

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing